Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a respiratory virus capable of infecting humans and causing mild to severe complications during and after infection, which collectively comprise coronavirus disease 2019 (COVID-19). After an initial local epidemic in
...
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a respiratory virus capable of infecting humans and causing mild to severe complications during and after infection, which collectively comprise coronavirus disease 2019 (COVID-19). After an initial local epidemic in late 2019, the virus quickly spread on a global scale and was declared a pandemic shortly after. Many research efforts were devoted to SARS-CoV-2 leading to the quick discovery and communication of crucial data, resulting in improved countermeasures and accelerated development and deployment of new vaccines. These achievements notwithstanding, a number of unknowns of the working mechanisms of the virus and its replication inside of a host still remain. The exact function and structure of the nucleocapsid (N) protein have not been clearly established despite its recognized importance throughout the virus’ life cycle. N is involved in both the replication and translation of viral RNA, although its most prominent function is the formation of ribonucleoprotein (RNP) for the stable and compact storage of genomic RNA inside virions. Here we present a course-grained model of N for molecular dynamics simulations. Employing simple rules, the dimerisation and RNA-binding capacities of N have been emulated. A range of parameters giving rise to structures resembling those found in vivo by balancing attractive and repulsive properties are analysed and described. Lastly, by implementing an RNA substitute, conformations have been found which could give an indication of the structure of the RNP found inside SARS-CoV-2 virions. The model described in this work can be used as a basis for more extensive simulations incorporating further elements to gain a better understanding of the behaviour of this and similar viruses, contributing to the prevention of future large-scale disease outbreaks.